<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"> <style>
	.KEYW {color: #933;}
	.COMM {color: #bbb; font-style: italic;}
	.NUMB {color: #393;}
	.STRN {color: #393;}
	.REGX {color: #339;}
	.line {border-right: 1px dotted #666; color: #666; font-style: normal;}
	</style></head><body><pre><span class='line'>  1</span> <span class="COMM">/**
<span class='line'>  2</span>  * Modified version of the original contract function for removing unnecessary
<span class='line'>  3</span>  * nodes while traversing the graph.
<span class='line'>  4</span>  * TODO: NOT USED
<span class='line'>  5</span>  * @param node node to contract the graph from
<span class='line'>  6</span>  * @param opt options
<span class='line'>  7</span>  */</span><span class="WHIT">
<span class='line'>  8</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">contractForTraversal</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">opt</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>  9</span> </span><span class="WHIT">	</span><span class="NAME">console.log</span><span class="PUNC">(</span><span class="STRN">"contractForTraversal"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 10</span> </span><span class="WHIT">	</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">viz</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">this.viz</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 11</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">node.collapsed</span><span class="WHIT"> </span><span class="PUNC">||</span><span class="WHIT"> </span><span class="PUNC">!</span><span class="NAME">node.anySubnode</span><span class="PUNC">(</span><span class="NAME">$jit.util.lambda</span><span class="PUNC">(</span><span class="KEYW">true</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="KEYW">return</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 12</span> </span><span class="WHIT">	</span><span class="NAME">opt</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">$jit.util.merge</span><span class="PUNC">(</span><span class="NAME">this.options</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">viz.config</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">opt</span><span class="WHIT"> </span><span class="PUNC">||</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 13</span> </span><span class="WHIT">		</span><span class="STRN">'modes'</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="PUNC">[</span><span class="STRN">'node-property:alpha:span'</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="STRN">'linear'</span><span class="PUNC">]</span><span class="WHIT">
<span class='line'> 14</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 15</span> </span><span class="WHIT">	</span><span class="NAME">node.collapsed</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 16</span> </span><span class="WHIT">	</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 17</span> </span><span class="WHIT">		</span><span class="NAME">n.eachSubnode</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 18</span> </span><span class="WHIT">			</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">ch.traversalTag</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 19</span> </span><span class="WHIT">				</span><span class="NAME">ch.ignore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 20</span> </span><span class="WHIT">				</span><span class="NAME">ch.setData</span><span class="PUNC">(</span><span class="STRN">'alpha'</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NUMB">0</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">opt.type</span><span class="WHIT"> </span><span class="PUNC">==</span><span class="WHIT"> </span><span class="STRN">'animate'</span><span class="PUNC">?</span><span class="WHIT"> </span><span class="STRN">'end'</span><span class="WHIT"> </span><span class="PUNC">:</span><span class="WHIT"> </span><span class="STRN">'current'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 21</span> </span><span class="WHIT">				</span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 22</span> </span><span class="WHIT">			</span><span class="PUNC">}</span><span class="WHIT">   
<span class='line'> 23</span> 		</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 24</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 25</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">opt.type</span><span class="WHIT"> </span><span class="PUNC">==</span><span class="WHIT"> </span><span class="STRN">'animate'</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 26</span> </span><span class="WHIT">		</span><span class="NAME">viz.compute</span><span class="PUNC">(</span><span class="STRN">'end'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 27</span> </span><span class="WHIT">		</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 28</span> </span><span class="WHIT">			</span><span class="NAME">n.eachSubnode</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 29</span> </span><span class="WHIT">				</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">ch.traversalTag</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 30</span> </span><span class="WHIT">					</span><span class="NAME">ch.setPos</span><span class="PUNC">(</span><span class="NAME">node.getPos</span><span class="PUNC">(</span><span class="STRN">'end'</span><span class="PUNC">)</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="STRN">'end'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 31</span> </span><span class="WHIT">					</span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 32</span> </span><span class="WHIT">				</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 33</span> </span><span class="WHIT">			</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 34</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 35</span> </span><span class="WHIT">		</span><span class="NAME">viz.fx.animate</span><span class="PUNC">(</span><span class="NAME">opt</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 36</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT"> 
<span class='line'> 37</span> 	</span><span class="KEYW">else</span><span class="WHIT"> </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">opt.type</span><span class="WHIT"> </span><span class="PUNC">==</span><span class="WHIT"> </span><span class="STRN">'replot'</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 38</span> </span><span class="WHIT">		</span><span class="NAME">viz.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 39</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 40</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 41</span> 
<span class='line'> 42</span> </span><span class="COMM">/** not used */</span><span class="WHIT">
<span class='line'> 43</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">deleteByBitscore</span><span class="PUNC">(</span><span class="NAME">bitscoreLimit</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 44</span> 
<span class='line'> 45</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 46</span> 
<span class='line'> 47</span> </span><span class="COMM">/** Function for deleting nodes from the graph.
<span class='line'> 48</span>  * If bitscoreLimit is not defined, all untagged nodes except root will be deleted.
<span class='line'> 49</span>  * If bitscoreLimit is defined, all untagged nodes (except root) without connections 
<span class='line'> 50</span>  * over that bitscore will be deleted. It will also preserve a path to root from each
<span class='line'> 51</span>  * remaining node (since many operations would break if graph became disconnected).
<span class='line'> 52</span>  *
<span class='line'> 53</span>  * Function will also clean all edges to (and from) the deleted nodes from the graph, 
<span class='line'> 54</span>  * and update data.bitscore field for remaining nodes.
<span class='line'> 55</span>  *
<span class='line'> 56</span>  * Will also untag all nodes once finished.
<span class='line'> 57</span>  * @param bitscoreLimit the limit under which nodes will be deleted
<span class='line'> 58</span>  */</span><span class="WHIT">
<span class='line'> 59</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">deleteUntagged</span><span class="PUNC">(</span><span class="NAME">bitscoreLimit</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 60</span> </span><span class="WHIT">	</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">nodesArray</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="PUNC">[</span><span class="PUNC">]</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 61</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.graph.eachBFS</span><span class="PUNC">(</span><span class="NAME">rgraph.root</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="NAME">nodesArray.push</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 62</span> </span><span class="WHIT">	</span><span class="COMM">// Add nodes to end of array and pop from there to get reverse-BFS order</span><span class="WHIT">
<span class='line'> 63</span> </span><span class="WHIT">	</span><span class="KEYW">while</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">nodesArray.length</span><span class="WHIT"> </span><span class="PUNC">></span><span class="WHIT"> </span><span class="NUMB">1</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 64</span> </span><span class="WHIT">		</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">node</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">nodesArray.pop</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 65</span> </span><span class="WHIT">		</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">&&</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">bitscoreLimit</span><span class="WHIT"> </span><span class="PUNC">||</span><span class="WHIT"> </span><span class="NAME">node.data.bitscore</span><span class="WHIT"> </span><span class="PUNC">&lt;</span><span class="WHIT"> </span><span class="NAME">bitscoreLimit</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 66</span> </span><span class="WHIT">			</span><span class="NAME">rgraph.op.removeNode</span><span class="PUNC">(</span><span class="WHIT">
<span class='line'> 67</span> </span><span class="WHIT">				</span><span class="NAME">node.id</span><span class="PUNC">,</span><span class="WHIT"> 
<span class='line'> 68</span> 				</span><span class="NAME">$jit.util.merge</span><span class="PUNC">(</span><span class="NAME">rgraph.op.userOptions</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 69</span> </span><span class="WHIT">					</span><span class="NAME">onComplete</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="NAME">cleanupGraph</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">colorEdges</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">updateBitscores</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 70</span> </span><span class="WHIT">					</span><span class="NAME">onAfterPlotNode</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="NAME">n.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">false</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 71</span> </span><span class="WHIT">			</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 72</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 73</span> </span><span class="WHIT">		</span><span class="KEYW">else</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 74</span> </span><span class="WHIT">			</span><span class="NAME">tagParents</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 75</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 76</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 77</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 78</span> 
<span class='line'> 79</span> </span><span class="COMM">/** Function for updating data.bitscore field for all nodes in the graph.
<span class='line'> 80</span>  * Should be used after deleting edges from the graph if relevant values are not otherwise updated.
<span class='line'> 81</span>  */</span><span class="WHIT">
<span class='line'> 82</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">updateBitscores</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 83</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.graph.eachNode</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 84</span> </span><span class="WHIT">		</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">bitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NUMB">0</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 85</span> </span><span class="WHIT">		</span><span class="NAME">node.eachAdjacency</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">edge</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 86</span> </span><span class="WHIT">			</span><span class="NAME">console.log</span><span class="PUNC">(</span><span class="NAME">edge</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 87</span> </span><span class="WHIT">			</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">edge.data.bitscore</span><span class="WHIT"> </span><span class="PUNC">></span><span class="WHIT"> </span><span class="NAME">bitscore</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 88</span> </span><span class="WHIT">				</span><span class="NAME">bitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">edge.data.bitscore</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 89</span> </span><span class="WHIT">			</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 90</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 91</span> </span><span class="WHIT">		</span><span class="NAME">node.data.bitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">bitscore</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 92</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 93</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 94</span> 
<span class='line'> 95</span> </span><span class="COMM">/** Function for checking if node has a tagged path to the root node.
<span class='line'> 96</span>  * Assumes the node has a path to root.
<span class='line'> 97</span>  * @param node the node for which to check the path
<span class='line'> 98</span>  */</span><span class="WHIT">
<span class='line'> 99</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>100</span> </span><span class="WHIT">	</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">parentNodes</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">node.getParents</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>101</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">parentNodes.length</span><span class="WHIT"> </span><span class="PUNC">==</span><span class="WHIT"> </span><span class="NUMB">0</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>102</span> </span><span class="WHIT">		</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">node.id</span><span class="WHIT"> </span><span class="PUNC">===</span><span class="WHIT"> </span><span class="NAME">rgraph.root</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>103</span> </span><span class="WHIT">		</span><span class="KEYW">else</span><span class="WHIT"> </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">false</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>104</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>105</span> </span><span class="WHIT">	</span><span class="KEYW">for</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">i</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NUMB">0</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">i</span><span class="WHIT"> </span><span class="PUNC">&lt;</span><span class="WHIT"> </span><span class="NAME">parentNodes.length</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">i</span><span class="PUNC">++</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>106</span> </span><span class="WHIT">		</span><span class="NAME">pnode</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">parentNodes</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="WHIT">
<span class='line'>107</span> </span><span class="WHIT">		</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">pnode.traversalTag</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="KEYW">continue</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>108</span> </span><span class="WHIT">		</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">pnode</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>109</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>110</span> </span><span class="WHIT">	</span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">false</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>111</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>112</span> 
<span class='line'>113</span> </span><span class="COMM">/** Function for tagging a node. If node has no tagged path to root, a path will also be tagged
<span class='line'>114</span>  * since otherwise deletion could result in disconnected graph.
<span class='line'>115</span>  * @param node the node to be tagged
<span class='line'>116</span>  */</span><span class="WHIT">
<span class='line'>117</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">tagNode</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>118</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="NAME">tagParents</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>119</span> </span><span class="WHIT">	</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>120</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT">
<span class='line'>121</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>122</span> 
<span class='line'>123</span> </span><span class="COMM">/** Function for tagging a path from node to root.
<span class='line'>124</span>  * Builds path by tagging the parent with the best (bitscore) connection to current node.
<span class='line'>125</span>  * Responsibility for updating the visualization is left to user, this function does
<span class='line'>126</span>  * not call refresh() or any animating function.
<span class='line'>127</span>  * @param node the node which will have its parents tagged
<span class='line'>128</span>  */</span><span class="WHIT">
<span class='line'>129</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">tagParents</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>130</span> </span><span class="WHIT">	</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">currentNode</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">node</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>131</span> </span><span class="WHIT">	</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">parents</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">node.getParents</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>132</span> </span><span class="WHIT">	</span><span class="KEYW">while</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">parents.length</span><span class="WHIT"> </span><span class="PUNC">></span><span class="WHIT"> </span><span class="NUMB">0</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>133</span> </span><span class="WHIT">		</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">bestParent</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">parents</span><span class="PUNC">[</span><span class="NUMB">0</span><span class="PUNC">]</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>134</span> </span><span class="WHIT">		</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">bestBitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">currentNode.getAdjacency</span><span class="PUNC">(</span><span class="NAME">parents</span><span class="PUNC">[</span><span class="NUMB">0</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">id</span><span class="PUNC">)</span><span class="PUNC">.</span><span class="NAME">data.bitscore</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>135</span> </span><span class="WHIT">		</span><span class="KEYW">for</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">i</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NUMB">1</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">i</span><span class="WHIT"> </span><span class="PUNC">&lt;</span><span class="WHIT"> </span><span class="NAME">parents.length</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="NAME">i</span><span class="PUNC">++</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>136</span> </span><span class="WHIT">			</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">tempBitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">currentNode.getAdjacency</span><span class="PUNC">(</span><span class="NAME">parents</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">id</span><span class="PUNC">)</span><span class="PUNC">.</span><span class="NAME">data.bitscore</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>137</span> </span><span class="WHIT">			</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">tempBitscore</span><span class="WHIT"> </span><span class="PUNC">></span><span class="WHIT"> </span><span class="NAME">bestBitscore</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>138</span> </span><span class="WHIT">				</span><span class="NAME">bestParent</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">parents</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>139</span> </span><span class="WHIT">				</span><span class="NAME">bestBitscore</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">tempBitscore</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>140</span> </span><span class="WHIT">			</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>141</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>142</span> </span><span class="WHIT">		</span><span class="NAME">bestParent.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>143</span> </span><span class="WHIT">		</span><span class="NAME">currentNode</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">bestParent</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>144</span> </span><span class="WHIT">		</span><span class="NAME">parents</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">currentNode.getParents</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>145</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>146</span> </span><span class="WHIT">	</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>147</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>148</span> 
<span class='line'>149</span> </span><span class="COMM">/** Tags the subnodes of the node
<span class='line'>150</span>  * @param node target node to have subnodes tagged*/</span><span class="WHIT">
<span class='line'>151</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">tagSubnodes</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>152</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="NAME">tagParents</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>153</span> </span><span class="WHIT">	</span><span class="NAME">node.eachSubnode</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">child</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>154</span> </span><span class="WHIT">		</span><span class="NAME">child.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>155</span> </span><span class="WHIT">		</span><span class="NAME">console.log</span><span class="PUNC">(</span><span class="STRN">"Child "</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="NAME">child.id</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="STRN">" tagged"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>156</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>157</span> </span><span class="WHIT">	</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>158</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT">
<span class='line'>159</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>160</span> 
<span class='line'>161</span> </span><span class="COMM">/** Tags the subgraph of the node
<span class='line'>162</span>  * @param node target node to have its subgraph tagged*/</span><span class="WHIT">
<span class='line'>163</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">tagSubgraph</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>164</span> </span><span class="WHIT">	</span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="NAME">tagParents</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>165</span> </span><span class="WHIT">	</span><span class="NAME">node.eachSubgraph</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">child</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>166</span> </span><span class="WHIT">		</span><span class="NAME">child.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>167</span> </span><span class="WHIT">		</span><span class="NAME">console.log</span><span class="PUNC">(</span><span class="STRN">"Child "</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="NAME">child.id</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="STRN">" tagged"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>168</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>169</span> </span><span class="WHIT">	</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>170</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT">
<span class='line'>171</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>172</span> 
<span class='line'>173</span> </span><span class="COMM">/** Untags a node.
<span class='line'>174</span>  * Since many operations rely on all nodes having a path to root, also untags all
<span class='line'>175</span>  * tagged nodes without a tagged path to root after untagging this node.
<span class='line'>176</span>  * @param node node to be untagged
<span class='line'>177</span>  */</span><span class="WHIT">
<span class='line'>178</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">untagNode</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>179</span> </span><span class="WHIT">	</span><span class="NAME">node.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">false</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>180</span> </span><span class="WHIT">	</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">n</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>181</span> </span><span class="WHIT">		</span><span class="NAME">n.eachSubnode</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>182</span> </span><span class="WHIT">			</span><span class="NAME">ch.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">checkRootTagpath</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>183</span> </span><span class="WHIT">			</span><span class="NAME">subn</span><span class="PUNC">(</span><span class="NAME">ch</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>184</span> </span><span class="WHIT">		</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>185</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>186</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT">
<span class='line'>187</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>188</span> 
<span class='line'>189</span> </span><span class="COMM">/** Untags a subgraph
<span class='line'>190</span>  *@param node node to have its subgraph untagged*/</span><span class="WHIT">
<span class='line'>191</span> </span><span class="KEYW">function</span><span class="WHIT"> </span><span class="NAME">untagSubgraph</span><span class="PUNC">(</span><span class="NAME">node</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>192</span> </span><span class="WHIT">	</span><span class="NAME">node.eachSubgraph</span><span class="PUNC">(</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">sn</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>193</span> </span><span class="WHIT">		</span><span class="NAME">sn.traversalTag</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="KEYW">false</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>194</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>195</span> </span><span class="WHIT">	</span><span class="NAME">rgraph.refresh</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="WHIT">
<span class='line'>196</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>197</span> 
<span class='line'>198</span> </span></pre></body></html>